CondaUpgradeError: This environment has previously been operated on by a conda version that's newer
than the conda currently being used. A newer version of conda is required.
target environment location: C:\Users\XXXXXXXXXX\AppData\Local\Continuum\anaconda3
current conda version: 4.5.11
minimum conda version: 4.6
Ok, let's try something stupid...
C:\Users\XXXXXXXX>pip install conda==4.6
Collecting conda==4.6
Could not find a version that satisfies the requirement conda==4.6 (from versions: 3.0.6, 3.5.0, 3.7.0, 3.17.0, 4.0.0, 4.0.1, 4.0.2, 4.0.3, 4.0.4, 4.0.5, 4.0.7, 4.0.8, 4.0.9, 4.1.2, 4.1.6, 4.2.6, 4.2.7, 4.3.13, 4.3.16)
No matching distribution found for conda==4.6
How do I get out of this trap? I've tried to upgrade it with various conda install and conda update commands but nothing works. This apparently happened upgrading from 4.6 to 4.6.2
Its a bug. recommendations are posted here on the conda issue board
basically, reinstall from cache or downgrade, then upgrade conda
Related
after using conda extensively for a while, I was asked to update it yesterday and now things look broken. I have to admit that I am not an expert of what goes on behind the scenes so bear with me :)
After installing conda I used pip to install the various packages.
Yesterday I started working on some code from a tutorial on git, which suggested to create an ad-hoc environment to work with:
conda env create -f binder/environment.yml
At this step I was suggested to update conda, since I was using an old version. I can't find in my terminal that specific message (i.e. I can't find what version of conda I was using before), but here is what I get now when I check the version of conda:
(base) francesco ~$ conda list conda
# packages in environment at /Users/francesco/anaconda3:
#
# Name Version Build Channel
_anaconda_depends 2019.03 py36_0
anaconda custom py36_1
anaconda-client 1.7.2 py36_0
anaconda-navigator 1.8.7 py36_0
anaconda-project 0.8.4 py_0
conda 4.8.3 py36_0
conda-build 3.10.5 py36_0
conda-env 2.6.0 h36134e3_0
conda-package-handling 1.6.0 py36h1de35cc_0
conda-verify 3.4.2 py_1
One of the things I noticed after the update is that in order to activate/deactivate the environment I had to use conda activate/deactivate <env> instead of source activate/deactivate <env>.
After that I worked with the code in the new environment without any problem.
Today I tried to activate the main environment I work with, but I was asked to "init" my shell first with:
conda init bash
After that I activated my "usual" environment:
conda activate testenv
and I tried to start Jupyter Lab, but I got this error:
(testenv) francesco ~$ jupyter lab
Error executing Jupyter command 'lab': [Errno 2] No such file or directory
What is happening? Why is Jupyter Lab not working anymore in my usual environment?
I checked the installation in testenv and things look ok:
(testenv) francesco ~$ conda list | grep jup
jupyter 1.0.0 py37_7
jupyter_client 5.2.4 py37_0
jupyter_console 6.0.0 py37_0
jupyter_core 4.4.0 py37_0
(testenv) francesco ~$ pip list | grep jup
jupyter 1.0.0
jupyter-client 5.2.4
jupyter-console 6.0.0
jupyter-core 4.4.0
(testenv) francesco ~$
Does anyone know what is going on? This is a huge problem for me as conda/jupyter lab are the main tools I use for work :\
The common practice is to only install Jupyter in a single Conda environment (typically your base env if an Anaconda user), and always launch Jupyter from there. To use other Python envs in Jupyter, you need to install ipykernel in those envs, e.g.,
conda install -n testenv ipykernel
And, to avoid having to register your additional envs, it is recommended to install nb_conda_kernels in the env with Jupyter, e.g.,
conda install -n base nb_conda_kernels
As a side note, installing things with Pip can make environments unstable. I strongly recommend learning and adhering to the documented best practices.
#FrancescoLS It seems that you had perhaps an older version of Conda installed(?) as the CHANGELOG indicates that source activate was deprecated in favor of conda activate in Conda v4.4.0 (as is also noted in this "How to Get Ready for the Release of conda 4.4" post from Anaconda).
This really isn't an "answer" in any actionable way, but it seems that you are not alone in Conda update breaking people's environments.
superuser: Conda update conda does extra stuff and destroy my anaconda install
Conda Issue #8842: Conda Deletes All Modules During Update
there are lots more. :/
I think it is safe to say that keeping virtual environments safely intact during an upgrade is hard to do, and that when doing a major upgrade across virtual environment maintainers (Conda) it is even harder. This is one of the reasons that I personally try to have all of my project virtual environments be maintained either in native Python 3 venv virtual environments with pip or through Poetry (as they are (or at least used to be) way faster to restore than having to go through Conda's slower solver) and then only resorting to using Conda when I need to bring in multiple external binary applications.
Were you able to make a new Conda environment for your work that effectively restores it (perhaps from your own environment.yml file for that environment)?
I have been having issues after updating conda to 4.6.9 and tried to downgrade to 4.6.8 by running
conda install conda=4.6.8 within my preferred conda env.
When I check the version via conda --version, however, I notice that the version is still 4.6.9.
Is there something else I need to do to get downgrade conda?
Running this on Windows.
The solution was to downgrade conda while in base environment and not my preferred environment.
I just installed Anaconda on a Windows 10 machine and the first thing I did thereafter was go into the Anaconda Prompt and run conda udpate conda and then conda update --all. As expected, it updated a lot of stuff. When I then ran Spyder, however, I got a pop-up saying that a new version of Spyder was available.
What? I just updated everything. Checking conda list I see that sypder 3.2.4 is indeed installed, so I do the following:
(base) C:\Users\Mark>conda update --all
Solving environment: done
All requested packages already installed.
(base) C:\Users\Mark>conda update spyder
Solving environment: done
Package Plan
environment location: C:\Users\Mark\Anaconda3
added / updated specs:
- spyder
The following packages will be downloaded:
package | build
---------------------------|-----------------
spyder-3.2.6 | py36_0 2.6 MB
The following packages will be UPDATED:
spyder: 3.2.4-py36h8845eaa_0 --> 3.2.6-py36_0
Proceed ([y]/n)?
Why is conda update -all not finding and updating my installed version of Spyder?
Have you tried just updating spyder?
conda update spyder
I had some similar behavior (on Linux) with conda, there it helped to be more specific:
conda update spyder=3.2.6
"NOTE: Conda updates to the highest version in its series, so Python 2.7 updates to the highest available in the 2.x series and 3.6 updates to the highest available in the 3.x series."
documentation conda
Try:
conda update -n base conda
Here, base is my current environment
I have a problem with using rpy2 on Anaconda Python. The issue is that it fails to import due to the following TypeError:
TypeError: type 'rpy2.rinterface.StrSexpVector' is not an acceptable
base type
My python version is 3.5, my anaconda version is 4.0.0, my rpy2 version is 2.7.0.
The problem seems to be that Anaconda now uses version 3.5 which is not compatible with rpy2 2.7.3 or lower, see https://bitbucket.org/rpy2/rpy2/issues/313/typeerror-type-rpy2rinterfacestrsexpvector - as Anaconda currently default installs 2.7.0 the import fails. How can this issue be fixed?
The issue is similar to the one asked here, Error when loading rpy2 with anaconda, however, the old solution of installing 2.7.0 is no longer compatible as explained above.
If you happen to be on OS X, I've built Conda packages for rpy2 2.8.0 which you can get with:
conda install -c ijstokes rpy2=2.8.0
These are available for Python 2.7 and 3.5. The problem stems from this rpy2 bug which has now been fixed: https://bitbucket.org/rpy2/rpy2/issues/313/typeerror-type-rpy2rinterfacestrsexpvector
If you're not on OS X, then you can build your own version with something like:
conda skeleton pypi rpy2 --version=2.8.0 --python=3.5
conda build rpy2
conda install --use-local rpy2
Those commands are from memory, but they should work or be close enough you can figure out the exact options.
I have installed python and many other useful tools on my Ubuntu 14.04 using Anaconda. I installed pysam (htslib interface for python) using
conda install pysam
However this installs the old version (0.6). The current version is 0.8.4. How can I install that version using conda. I don't want to use pip install pysam because I read somewhere it might cause problems.
Thanks.
Anaconda only provides version 0.6. You can install from binstar with:
conda install -c https://conda.anaconda.org/uhlitz pysam
This should give you version 0.8.3 for linux64. Other channels are also available.